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O-glycosylation of the mucin type.

While only about ten percent of the databank entries are defined as glycoproteins, it has been estimated recently that more than half of all proteins are glycoproteins. Mucin-type O-glycosylation is a widespread post-translational modification of proteins found in the entire animal kingdom, but also in higher plants. The structural complexity of the chains initiated by O-linked GalNAc exceeds that of N-linked chains by far. The process during which serine and threonine residues of proteins become modified is confined to the cis to trans Golgi compartments. The initiation of this process by peptidyl GalNAc-transferases is ruled by the sequence context of putative O-glycosylation sites, but also by epigenetic regulatory mechanisms, which can be mediated by enzyme competition. The cellular repertoir of glycosyltransferases with their distinct donor sugar and acceptor sugar specificities, their sequential action at highly-ordered surfaces, and their localizations in subcompartments of the Golgi finally determine the cell-specific O-glycosylation profile. Dramatic alterations of the glycosylation machinery are observed in cancer cells, resulting in aberrantly O-glycosylated proteins that expose previously masked peptide motifs and new antigenic targets. The functional aspects of O-linked glycans, which comprise among many others their potential role in sorting and secretion of glycoproteins, their influence on protein conformation, and their multifarious involvement in cell adhesion and immunological processes, appear as complex as their structures.

Animals↗

[Characteristics of biogenesis and substrate specificity of lysosomal glycosidases under normal conditions and in glycosidoses].

Main steps are considered of posttranslational modification of lysosomal hydrolases, which are glycoproteins. Processing of the enzymatic carbohydrate moiety in various compartments of endoplasmic reticulum and Golgi apparatus is discussed. Importance of mannose-6-phosphate groups formed during the processing is revealed by studies on binding of these enzymes with specific receptor responsible for their transport into lysosomes. Specificity of lysosomal glycosidases and their isoforms, catalyzing hydrolysis of carbohydrate chains of glycoconjugates and of synthetic substrates dissimilar in the structure, is discussed. Complex structural organization of these enzymes in lysosomes (protein activators and stabilizing factors, presence of marker sites etc) was studied using as an example lysosomal diseases of accumulation, glycosidoses, developed in hereditary deficiency of glycosidases. The data on elevated activity of the majority of lysosomal enzymes in glycosidoses, which are not involved in the primary genetic defect, suggest the possibility of general unspecific response of cells to accumulation of unhydrolyzed compounds.

Glycoside Hydrolases↗

Molecular recognition with C-clamp porphyrins: synthesis, structural, and complexation studies.

Porphyrin-based molecular clefts equipped with a strategically positioned carboxylic group have been synthesized. These ditopic porphyrins exhibit excellent binding affinity for many neutral substrates. X-ray structures of a porphyrin-water inclusion complex and a Zn(porphyrin)-methanol complex reveal how the carboxylic group interacts with substrates via H-bonding. Multipoint recognition is demonstrated in the differential binding of 1,2,3- versus 1,2,4-triazole, suggesting the possible use of such receptors to separate heterocyclic bases.

Crystallography, X-Ray↗

Structural insight into antibiotic fosfomycin biosynthesis by a mononuclear iron enzyme.

The biosynthetic pathway of the clinically important antibiotic fosfomycin uses enzymes that catalyse reactions without precedent in biology. Among these is hydroxypropylphosphonic acid epoxidase, which represents a new subfamily of non-haem mononuclear iron enzymes. Here we present six X-ray structures of this enzyme: the apoenzyme at 2.0 A resolution; a native Fe(II)-bound form at 2.4 A resolution; a tris(hydroxymethyl)aminomethane-Co(II)-enzyme complex structure at 1.8 A resolution; a substrate-Co(II)-enzyme complex structure at 2.5 A resolution; and two substrate-Fe(II)-enzyme complexes at 2.1 and 2.3 A resolution. These structural data lead us to suggest how this enzyme is able to recognize and respond to its substrate with a conformational change that protects the radical-based intermediates formed during catalysis. Comparisons with other family members suggest why substrate binding is able to prime iron for dioxygen binding in the absence of alpha-ketoglutarate (a co-substrate required by many mononuclear iron enzymes), and how the unique epoxidation reaction of hydroxypropylphosphonic acid epoxidase may occur.

Apoenzymes↗

Variation in the ordered structure of complexes between CD154 and anti-CD154 monoclonal antibodies.

The cell surface co-stimulatory protein CD154 (CD40L) is a target for monoclonal antibody (mAb) inhibitors of T-cell mediated immune diseases. This protein, like most other members of the TNF ligand family, forms homotrimeric complexes on the cell surface and in solution, with a three-fold axis of symmetry. We find that several different anti-CD154 monoclonal antibodies form distinctive complexes with soluble CD154. These soluble complexes have been analyzed using size exclusion chromatography, static and dynamic light scattering, and electron microscopy and shown to consist of caged structures of various geometries. The cell surface complexes have been analyzed by confocal microscopy and, depending on the mAb, remain as small, separate complexes or form large aggregates. The formation of these complexes in solution is likely to have an impact on measures of affinity, while the cell surface complexes could affect binding potency and provoke other biological effects.

Antibodies, Monoclonal↗

The nuclear pore complex: mediator of translocation between nucleus and cytoplasm.

The enclosure of nuclear contents in eukaryotes means that cells require sites in the boundary that mediate exchange of material between nucleus and cytoplasm. These sites, termed nuclear pore complexes (NPCs), number 100-200 in yeast, a few thousand in mammalian cells and approximately 50 million in the giant nuclei of amphibian oocytes. NPCs are large (125 MDa) macromolecular complexes that comprise 50-100 different proteins in vertebrates. In spite of their size and complex structure, NPCs undergo complete breakdown and reformation at cell division. Transport through NPCs can be rapid (estimated at several hundred molecules/pore/second) and accommodates both passive diffusion of relatively small molecules, and active transport of complexes up to several megadaltons in molecular mass. Each pore can facilitate both import and export. The two processes apparently involve multiple pathways for different cargoes, and their transport signals, transport receptors and adapters, and the molecules (and their regulators) that underpin the transport mechanisms. Over the past few years there has been an increasing interest in the pore complex: structural studies have been followed by elucidation of the biochemical aspects of nuclear import, and subsequent investigations into nuclear export. The current challenge is to understand the interactions between the structural elements of the pore complex and the mechanisms that drive the physical processes of translocation through it.

Animals↗

Heteroleptic copper dipyrromethene complexes: synthesis, structure, and coordination polymers.

The synthesis of neutral [Cu(dpm)2] and [Cu(dpm)(acac)] (dpm = dipyrromethene, acac = acetylacetonato) complexes is presented. The formation of the asymmetric metal complexes was monitored by electronic absorption and infrared spectroscopy. Two of the complexes investigated, containing pyrdpm ligands (pyrdpm = pyridyldipyrromethene), form 1-dimensional coordination polymers. The coordination polymers formed by these complexes have been characterized by single-crystal X-ray diffraction, differential scanning calorimetry, and thermogravimetric analysis. The complexes possess square pyramidal coordination geometries with the apical position occupied by the meso-pyridyl donor of a neighboring complex in the crystal lattice. The features of these coordination complexes that facilitate formation of extended solids have been probed. Symmetric [Cu(pyrdpm)2] complexes are unable to form coordination solids due to steric hindrance at the metal center. Use of cyano donors in complexes such as [Cu(cydpm)(acac)] (cydpm = cyanodipyrromethene) in lieu of pyridyl donors also fail to form network solids. Through these systematic studies, both the basic coordination chemistry of these complexes and the fundamental design requirements for synthesizing this novel class of coordination polymers have been defined.

Calorimetry, Differential Scanning↗

The nonspecific DNA-binding and -bending proteins HMG1 and HMG2 promote the assembly of complex nucleoprotein structures.

The mammalian high mobility group proteins HMG1 and HMG2 are abundant, chromatin-associated proteins whose cellular function is not known. In this study we show that these proteins can substitute for the prokaryotic DNA-bending protein HU in promoting the assembly of the Hin invertasome, an intermediate structure in Hin-mediated site-specific DNA inversion. Formation of this complex requires the assembly of the Hin recombinase, the Fis protein, and three cis-acting DNA sites, necessitating the looping of intervening DNA segments. Invertasome assembly is strongly stimulated by HU or HMG proteins when one of these segments is shorter than 104 bp. By use of ligase-mediated circularization assays, we demonstrate that HMG1 and HMG2 can bend DNA extremely efficiently, forming circles as small as 66 bp, and even 59-bp circles at high HMG protein concentrations. In both invertasome assembly and circularization assays, substrates active in the presence of HMG1 contain one less helical turn of DNA compared with substrates active in the presence of HU protein. Analysis of different domains of HMG1 generated by partial proteolytic digestion indicate that DNA-binding domain B is sufficient for both bending and invertasome assembly. We suggest that an important biological function of HMG1 and HMG2 is to facilitate cooperative interactions between cis-acting proteins by promoting DNA flexibility. A general role for HMG1 and HMG2 in chromatin structure is also suggested by their ability to wrap DNA duplexes into highly compact forms.

Animals↗

Acetylcholinesterase inhibition by fasciculin: crystal structure of the complex.

The crystal structure of the snake toxin fasciculin, bound to mouse acetylcholinesterase (mAChE), at 3.2 A resolution reveals a synergistic three-point anchorage consistent with the picomolar dissociation constant of the complex. Loop II of fasciculin contains a cluster of hydrophobic residues that interact with the peripheral anionic site of the enzyme and sterically occlude substrate access to the catalytic site. Loop I fits in a crevice near the lip of the gorge to maximize the surface area of contact of loop II at the gorge entry. The fasciculin core surrounds a protruding loop on the enzyme surface and stabilizes the whole assembly. Upon binding of fasciculin, subtle structural rearrangements of AChE occur that could explain the observed residual catalytic activity of the fasciculin-enzyme complex.

Animals↗

Substrate deformation in a hypoxanthine-guanine phosphoribosyltransferase ternary complex: the structural basis for catalysis.

BACKGROUND: Hypoxanthine-guanine phosphoribosyltransferases (HGPRTs) are well-recognized antiparasitic drug targets. HGPRT is also a paradigmatic representative of the phosphoribosyltransferase family of enzymes, which includes other important biosynthetic and salvage enzymes and drug targets. To better understand the reaction mechanism of this enzyme, we have crystallized HGPRT from the apicomplexan protozoan Toxoplasma gondii as a ternary complex with a substrate and a substrate analog. RESULTS: The crystal structure of T. gondii HGPRT with the substrate Mg2+-PRPP and a nonreactive substrate analog, 9-deazaguanine, bound in the active site has been determined at 1.05 A resolution and refined to a free R factor of 15.4%. This structure constitutes the first atomic-resolution structure of both a phosphoribosyltransferase and the central metabolic substrate PRPP. This pre-transition state complex provides a clearer understanding of the structural basis for catalysis by HGPRT. CONCLUSIONS: Three types of substrate deformation, chief among them an unexpected C2'-endo pucker adopted by the PRPP ribose ring, raise the energy of the ground state. A cation-pi interaction between Tyr-118 and the developing oxocarbenium ion in the ribose ring helps to stabilize the transition state. Enforced substrate propinquity coupled with optimal reactive geometry for both the substrates and the active site residues with which they interact contributes to catalysis as well.

Animals↗

Catalytically active MAP KAP kinase 2 structures in complex with staurosporine and ADP reveal differences with the autoinhibited enzyme.

MAP KAP kinase 2 (MK2), a Ser/Thr kinase, plays a crucial role in the inflammatory process. We have determined the crystal structures of a catalytically active C-terminal deletion form of human MK2, residues 41-364, in complex with staurosporine at 2.7 A and with ADP at 3.2 A, revealing overall structural similarity with other Ser/Thr kinases. Kinetic analysis reveals that the K(m) for ATP is very similar for MK2 41-364 and p38-activated MK2 41-400. Conversely, the catalytic rate and binding for peptide substrate are dramatically reduced in MK2 41-364. However, phosphorylation of MK2 41-364 by p38 restores the V(max) and K(m) for peptide substrate to values comparable to those seen in p38-activated MK2 41-400, suggesting a mechanism for regulation of enzyme activity.

Adenosine Diphosphate↗

A complex photoreceptive structure in the cyanobacterium Leptolyngbya sp.

Among the terrestrial epilithic cyanobacteria isolated from Roman hypogea at extremely low light intensity, a non-heterocystous strain, belonging to the genus Leptolyngbya, showed a marked photobehavior. These red cyanobacteria possess an orange spot at the tip of the apical cell. Micro-spectrophotometric analysis of this tip showed an absorption spectrum with two bands, centered at 456 and 504 nm, respectively. Experiments on photo-orientation impairment of these cells, and micro-spectrophotometric analysis of the tip of impaired trichomes showed that a rhodopsin-like protein might be present in this structure. All these data could support the hypothesis of the presence of a complex photoreceptive system in this prokaryote.

Bacterial Proteins↗

Synthesis, characterization and cytotoxicity of new platinum(IV) axial carboxylate complexes: crystal structure of potential antitumor agent [PtIV(trans-1R,2R-diaminocyclohexane)trans(acetate)2Cl2].

A series of new platinum(IV) complexes of the type [PtIV(DACH)trans(L)2Cl2] (where DACH = trans-1R,2R-diaminocyclohexane, and L = acetate, propionate, butyrate, valerate, hexanoate, or heptanoate) bearing the carboxylate groups in the axial positions have been synthesized and characterized by elemental analysis, IR, and 195Pt NMR spectroscopy. The crystal structure of the analogue [PtIV(DACH)trans(acetate)2Cl2] was determined by single crystal X-ray diffraction method. There were two crystallographically independent molecules, both of which lie on crystallographic two-fold axes. The bond lengths and bond angles of both the molecules were the same within the experimental error. The compound crystallizes in the monoclinic space group C2, with a = 11.180(2) A, b = 14.736(3) A, c = 10.644(2) A, beta = 112.38(3) degrees, Z = 4 and R = 0.0336, based upon a total of 1648 collected reflections. In this complex, the platinum had a slightly distorted octahedron geometry owing to the presence of a geometrically strained five-member ring. The two adjacent corners of the platinum plane were occupied by the two amino nitrogens of DACH, whereas the other two equatorial positions were occupied by two chloride ions. The remaining two axial positions were occupied by the oxygens of acetate ligands. The DACH ring was in a chair configuration. An intricate network of intermolecular hydrogen bonds held the crystal lattice together. These analogues were evaluated in vitro and demonstrated cytotoxic activity against the human ovarian 2008 tumor cell line (IC50 = 0.001-0.06 microM). Structure-activity study revealed that activity was highest for the analogue where L = butyrate.

Antineoplastic Agents↗

Novel copper(II)-dien-imidazole/imidazolate-bridged copper(II) complexes. Crystal structure of [Cu(dien)(Him)](ClO4)2 and of [(dien)Cu(mu-im)Cu(dien)](ClO4)3, a homobinuclear model for the copper(II) site of the CuZn-superoxide dismutase.

The imidazolate-bridged binuclear copper(II)-copper(II) complex [(dien)Cu(mu-im)Cu(dien)](ClO(4))(3) and related mononuclear complexes [Cu(dien)(H(2)O)](ClO(4))(2), [Cu(dien)(Him)](ClO(4))(2) were synthesized with diethylenetriamine (dien) as capping ligand. The crystal structure of mononuclear [Cu(dien)(Him)](ClO(4))(2) and binuclear complex [(dien)Cu(mu-im)Cu(dien)](ClO(4))(3) have been determined by single crystal X-ray diffraction methods. The mononuclear complex [Cu(dien)(Him)](ClO(4))(2) crystallizes in the orthorhombic, Pca2(1) with a = 9.3420(9) A, b = 12.3750(9) A, c = 14.0830(9) A, beta = 90.000(7)(o) and Z = 4 and binuclear complex [(dien)Cu(mu-im)Cu(dien)](ClO(4))(3) crystallizes in the monoclinic space group P2(1)/a, with a = 15.017(7) A, b = 11.938(6) A, c = 15.386(6) A, beta = 110.30(4)(o) and Z = 4. The molecular structures show that copper(II) ions in an asymmetrically elongated octahedral coordination (type 4 + 1 + 1) and in binuclear complex Cu(1) atom has a asymmetrically elongated octahedral coordination (type type 4 + 1 + 1) and Cu(2) atom exhibits a square base pyramidal coordination (type 4 + 1). The bridging ligand (imidazolate ion, im) lies nearly on a straight line between two Cu(2+), which are separated by 5.812 A, slightly shorter than the value in copper-copper superoxide dismutase (Cu(2)-Cu(2)SOD). Magnetic measurements and electron spin resonance (ESR) spectroscopy of the binuclear complex have shown an antiferromagnetic exchange interaction. From pH-dependent cyclic voltametry (CV) and electronic spectroscopic studies the complex has been found to be stable over a wide pH range (7.75-12.50).

Absorption↗

(Nitro)Iron(III) Porphyrins. EPR Detection of a Transient Low-Spin Iron(III) Complex and Structural Characterization of an O Atom Transfer Product.

The reaction of BF(3).OEt(2) with the bis(nitro) complex of iron(III) picket-fence porphyrin, [K(18C6)(OH(2))][Fe(TpivPP)(NO(2))(2)], leads to the formation of a transient porphyrin intermediate, assigned on the basis of its rhombic low-spin EPR spectrum as the five-coordinate N-bound mono(nitro) iron(III) derivative, [Fe(TpivPP)(NO(2))]. This species is reactive and readily undergoes oxygen atom transfer to form [Fe(III)(TpivPP)(NO(3))] and [Fe(II)(TpivPP)(NO)]. The reactions have been followed by EPR and IR spectroscopy. [Fe(TpivPP)(NO(2))] has a rhombic EPR spectrum (g = 2.60, 2.35, and 1.75) in chlorobenzene and CH(2)Cl(2) and is spectroscopically distinct from the bis(nitro) starting material (g = 2.70, 2.50, and 1.57). Oxidation of the nitrosyl species to [Fe(TpivPP)(NO(3))] proceeds via an intermediate assigned as [Fe(TpivPP)(NO(2))] on the basis of its EPR spectrum. The crystal structure of one of the reaction products, [Fe(TpivPP)(NO(3))], has been determined. The nitrate ion of [Fe(TpivPP)(NO(3))] is bound to the iron(III) ion in a "symmetric" bidentate fashion within the ligand-binding pocket of the porphyrin pickets. Individual Fe-O distances are 2.123(3) and 2.226(3) Å. The dihedral angle between the plane of the nitrate ion and the closest N(p)-Fe-N(p) plane is 10.0 degrees. The Fe-N(p) bonds (and trans N(p)-Fe-N(p) angles) perpendicular and parallel to the plane of the axial ligand average to 2.060(5) Å (154.84(9) degrees ) and 2.083(3) Å (146.14(9) degrees ), respectively. Crystal data for [Fe(TpivPP)(NO(3))]: a = 23.530(2) Å, b = 10.0822(5) Å, c = 48.748(3) Å, beta = 92.145(5) degrees, monoclinic, space group I2/a, V = 11556.4(14) Å(3), Z = 8, FeN(9)O(7)C(64)H(64), 8798 observed data, R(1) = 0.0606, wR(2) = 0.1313, all observations at 127(2) K.

Journal Article↗

Single-crystal-like diffraction data from polycrystalline materials

A method for solving structures from powder diffraction data was developed, and its validity was demonstrated on three complex structures. The method uses a textured sample and exploits the high intensity and parallel nature of synchrotron radiation. In principle, crystal structures as complex as those routinely solved by single-crystal methods can be determined with this approach. For example, the as-synthesized form of the zeolite UTD-1, with 69 nonhydrogen atoms in the asymmetric unit, could be solved directly. With this method, a larger range of structural complexity becomes accessible to scientists interested in the structures of polycrystalline materials that cannot be grown as single crystals.

Journal Article↗

Encapsulation of cyanometalates by a tris-macrocyclic ligand tricopper(II) complex: syntheses, structural variation, and magnetic exchange coupling pathways.

The reaction of [M(CN)(6)](3-) (M = Cr(3+), Mn(3+), Fe(3+), Co(3+)) and [M(CN)(8)](4-/3-) (M = Mo(4+/5+), W(4+/5+)) with the trinuclear copper(II) complex of 1,3,5-triazine-2,4,6-triyltris[3-(1,3,5,8,12-pentaazacyclotetradecane)] ([Cu(3)(L)](6+)) leads to partially encapsulated cyanometalates. With hexacyanometalate(III) complexes, [Cu(3)(L)](6+) forms the isostructural host-guest complexes [[[Cu(3)(L)(OH(2))(2)][M(CN)(6)](2)][M(CN)(6)]][M(CN)(6)]30 H(2)O with one bridging, two partially encapsulated, and one isolated [M(CN)(6)](3-) unit. The octacyanometalates of Mo(4+/5+) and W(4+/5+) are encapsulated by two tris-macrocyclic host units. Due to the stability of the +IV oxidation state of Mo and W, only assemblies with [M(CN)(8)](4-) were obtained. The Mo(4+) and W(4+) complexes were crystallized in two different structural forms: [[Cu(3)(L)(OH(2))](2)[Mo(CN)(8)]](NO(3))(8)15 H(2)O with a structural motif that involves isolated spherical [[Cu(3)(L)(OH(2))](2)[M(CN)(8)]](8+) ions and a "string-of-pearls" type of structure [[[Cu(3)(L)](2)[M(CN)(8)]][M(CN)(8)]](NO(3))(4) 20 H(2)O, with [M(CN)(8)](4-) ions that bridge the encapsulated octacyanometalates in a two-dimensional network. The magnetic exchange coupling between the various paramagnetic centers is characterized by temperature-dependent magnetic susceptibility and field-dependent magnetization data. Exchange between the CuCu pairs in the [Cu(3)(L)](6+) "ligand" is weakly antiferromagnetic. Ferromagnetic interactions are observed in the cyanometalate assemblies with Cr(3+), exchange coupling of Mn(3+) and Fe(3+) is very small, and the octacoordinate Mo(4+) and W(4+) systems have a closed-shell ground state.

Journal Article↗

[The structure of complex carbohydrate chains of hemagglutinin from influenza viruses A/Kiev/59/79 (H1N1), A/Chile/1/83/25(H1N1) and X/79(H3N2)].

An earlier developed method of identification of oligosaccharides by HPLC was used for studying the carbohydrate chains of three hemagglutinins from various influenza virus strains. The structures of main oligosaccharides of the complex type were elucidated on the basis of their chromatographic characteristics and monosaccharide composition. Oligosaccharide patterns varied in the above hemagglutinin samples but in all cases the major complex chains were fucosylated and nonfucosylated biatennary chains; bisected and triantennary chains were also found.

Carbohydrates↗